The story begins with a cloaked person surveying a wasteland. The person says that someone named Star is bound to be heading towards the past to fix all this chaos. After picking up a watch, the person turns the handles back, and is sent a few million years into the past.

Back in the present, Sonic is going after Eggman, who wishes to find the seven Chaos Emeralds (all of which were left in special chambers and eventually forgotten). Eggman gets his hands on the green Emerald, which is then stolen by a mysterious girl. She reveals her name - Star - before taking off with the Emerald. Sonic pursues her, but is then stopped by a mysterious robot called Zing she is supposedly controlling remotely. After its defeat, Zing goes berserk and attempts to take the Chaos Emerald, but is stopped by another, smaller humanoid robot.

Sonic pursues Star some more; however, he's stalled by a barrier separating the two. Star heads to a chamber with the humanoid, whose name is Raina, and takes the Emerald inside. Raina then asks what she wants to do with the Emerald, and Star reveals her motivation - to take the Emeralds and destroy them so that, in a few million years, no one will misuse them.